Recently, fibre-optical nonlinear endoscopy has been increasingly attractive for early recognition and diagnostics of gastrointestinal tract cancers due to the non-invasive, flexible and miniaturised feature. To reduce the volume of the system, several miniaturised scanning mechanisms have been employed, including a two-dimensional (2D) microelectromechanical system (MEMS) mirror [1] and a PZT actuator. However, these scanning devices only perform on one dimension or two dimensions. To achieve a three-dimensional (3D) imaging, another scanner such as a bulk one-dimensional (1D) scanning stage or an actuator is usually used to move samples axially which seriously obstructs the system size reduction and simplification. To overcome this disadvantage, a 3D MEMS mirror is applied for the 3D scanning in this paper. Figure 1 is the experimental setup for a 3D MEMS enabled fibre endoscope. A double-clad photonic crystal fibre (DC-PCF) is one of the key components for a compact endoscope because it has a large core for single-mode delivery of excitation laser beam and a large inner cladding with a high numerical aperture (NA) for efficient signal collection at separate wavelengths. To examine the effectiveness of the miniaturised endoscopic system, two-photon fluorescence images of 10 μm microspheres in three dimensions have been obtained at a laser excitation wavelength of 800 nm with a repetition rate of 80 MHz and a pulse width of 80 fs (Spectra Physics, Maitai).